feature/finegrain-region-read

bioio/bio_image.py

@@ -904,11 +904,20 @@ def get_image_data(
 
         See `bioio_base.transforms.reshape_data` for more details.
         """
-        # If no out orientation, simply return current data as dask array
+
+        # Determine if image needs to be stitched
+        stitching_mosaic = (
+            self._reconstruct_mosaic
+            and biob.dimensions.DimensionNames.MosaicTile in self.reader.dims.order
+        )
+        # direct reader sub-region read for kwarg slice. The only accepted kwargs
+        # is slice definitions so we can assert directly on their presence.
+        if dimension_order_out is not None and kwargs and not stitching_mosaic:
+            return self.reader.get_image_data(dimension_order_out, **kwargs)
+
+        # Otherwise read the full image: return it as-is, or reshape/slice it.
         if dimension_order_out is None and not kwargs:
             return self.data
-
-        # Transform and return
         return biob.transforms.reshape_data(
             data=self.data,
             given_dims=self.dims.order,

pyproject.toml

@@ -31,7 +31,7 @@ dynamic = ["version"]
 dependencies = [
   # We always pin a specific version of bioio-base with
   # each release so that we avoid bioio + bioio-base misalignment.
-  "bioio-base~=3.3.0",
+  "bioio-base~=3.4.0",
   "dask[array]>=2021.4.1",
   "numpy>=1.21.0",
   "ome-types[lxml]>=0.4.0",